/*
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 *    GreedyStepwise.java
 *    Copyright (C) 2004-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.attributeSelection;

import java.util.ArrayList;
import java.util.BitSet;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;

import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.RevisionUtils;
import weka.core.Utils;

/**
 <!-- globalinfo-start -->
 * GreedyStepwise :<br/>
 * <br/>
 * Performs a greedy forward or backward search through the space of attribute subsets. May start with no/all attributes or from an arbitrary point in the space. Stops when the addition/deletion of any remaining attributes results in a decrease in evaluation. Can also produce a ranked list of attributes by traversing the space from one side to the other and recording the order that attributes are selected.<br/>
 * <p/>
 <!-- globalinfo-end -->
 * 
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -C
 *  Use conservative forward search</pre>
 * 
 * <pre> -B
 *  Use a backward search instead of a
 *  forward one.</pre>
 * 
 * <pre> -P &lt;start set&gt;
 *  Specify a starting set of attributes.
 *  Eg. 1,3,5-7.</pre>
 * 
 * <pre> -R
 *  Produce a ranked list of attributes.</pre>
 * 
 * <pre> -T &lt;threshold&gt;
 *  Specify a theshold by which attributes
 *  may be discarded from the ranking.
 *  Use in conjuction with -R</pre>
 * 
 * <pre> -N &lt;num to select&gt;
 *  Specify number of attributes to select</pre>
 * 
 * <pre> -num-slots &lt;int&gt;
 *  The number of execution slots, for example, the number of cores in the CPU. (default 1)
 * </pre>
 * 
 * <pre> -D
 *  Print debugging output</pre>
 * 
 <!-- options-end -->
 * 
 * @author Mark Hall
 * @version $Revision: 9848 $
 */
public class GreedyStepwise extends ASSearch implements RankedOutputSearch,
    StartSetHandler, OptionHandler {

  /** for serialization */
  static final long serialVersionUID = -6312951970168325471L;

  /** does the data have a class */
  protected boolean m_hasClass;

  /** holds the class index */
  protected int m_classIndex;

  /** number of attributes in the data */
  protected int m_numAttribs;

  /** true if the user has requested a ranked list of attributes */
  protected boolean m_rankingRequested;

  /**
   * go from one side of the search space to the other in order to generate a
   * ranking
   */
  protected boolean m_doRank;

  /** used to indicate whether or not ranking has been performed */
  protected boolean m_doneRanking;

  /**
   * A threshold by which to discard attributes---used by the AttributeSelection
   * module
   */
  protected double m_threshold;

  /**
   * The number of attributes to select. -1 indicates that all attributes are to
   * be retained. Has precedence over m_threshold
   */
  protected int m_numToSelect = -1;

  protected int m_calculatedNumToSelect;

  /** the merit of the best subset found */
  protected double m_bestMerit;

  /** a ranked list of attribute indexes */
  protected double[][] m_rankedAtts;
  protected int m_rankedSoFar;

  /** the best subset found */
  protected BitSet m_best_group;
  protected ASEvaluation m_ASEval;

  protected Instances m_Instances;

  /** holds the start set for the search as a Range */
  protected Range m_startRange;

  /** holds an array of starting attributes */
  protected int[] m_starting;

  /** Use a backwards search instead of a forwards one */
  protected boolean m_backward = false;

  /**
   * If set then attributes will continue to be added during a forward search as
   * long as the merit does not degrade
   */
  protected boolean m_conservativeSelection = false;

  /** Print debugging output */
  protected boolean m_debug = false;

  protected int m_poolSize = 1;

  /** Thread pool */
  protected transient ExecutorService m_pool = null;

  /**
   * Constructor
   */
  public GreedyStepwise() {
    m_threshold = -Double.MAX_VALUE;
    m_doneRanking = false;
    m_startRange = new Range();
    m_starting = null;
    resetOptions();
  }

  /**
   * Returns a string describing this search method
   * 
   * @return a description of the search suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String globalInfo() {
    return "GreedyStepwise :\n\nPerforms a greedy forward or backward search "
        + "through "
        + "the space of attribute subsets. May start with no/all attributes or from "
        + "an arbitrary point in the space. Stops when the addition/deletion of any "
        + "remaining attributes results in a decrease in evaluation. "
        + "Can also produce a ranked list of "
        + "attributes by traversing the space from one side to the other and "
        + "recording the order that attributes are selected.\n";
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String searchBackwardsTipText() {
    return "Search backwards rather than forwards.";
  }

  /**
   * Set whether to search backwards instead of forwards
   * 
   * @param back true to search backwards
   */
  public void setSearchBackwards(boolean back) {
    m_backward = back;
    if (m_backward) {
      setGenerateRanking(false);
    }
  }

  /**
   * Get whether to search backwards
   * 
   * @return true if the search will proceed backwards
   */
  public boolean getSearchBackwards() {
    return m_backward;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String thresholdTipText() {
    return "Set threshold by which attributes can be discarded. Default value "
        + "results in no attributes being discarded. Use in conjunction with "
        + "generateRanking";
  }

  /**
   * Set the threshold by which the AttributeSelection module can discard
   * attributes.
   * 
   * @param threshold the threshold.
   */
  @Override
  public void setThreshold(double threshold) {
    m_threshold = threshold;
  }

  /**
   * Returns the threshold so that the AttributeSelection module can discard
   * attributes from the ranking.
   */
  @Override
  public double getThreshold() {
    return m_threshold;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String numToSelectTipText() {
    return "Specify the number of attributes to retain. The default value "
        + "(-1) indicates that all attributes are to be retained. Use either "
        + "this option or a threshold to reduce the attribute set.";
  }

  /**
   * Specify the number of attributes to select from the ranked list (if
   * generating a ranking). -1 indicates that all attributes are to be retained.
   * 
   * @param n the number of attributes to retain
   */
  @Override
  public void setNumToSelect(int n) {
    m_numToSelect = n;
  }

  /**
   * Gets the number of attributes to be retained.
   * 
   * @return the number of attributes to retain
   */
  @Override
  public int getNumToSelect() {
    return m_numToSelect;
  }

  /**
   * Gets the calculated number of attributes to retain. This is the actual
   * number of attributes to retain. This is the same as getNumToSelect if the
   * user specifies a number which is not less than zero. Otherwise it should be
   * the number of attributes in the (potentially transformed) data.
   */
  @Override
  public int getCalculatedNumToSelect() {
    if (m_numToSelect >= 0) {
      m_calculatedNumToSelect = m_numToSelect;
    }
    return m_calculatedNumToSelect;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String generateRankingTipText() {
    return "Set to true if a ranked list is required.";
  }

  /**
   * Records whether the user has requested a ranked list of attributes.
   * 
   * @param doRank true if ranking is requested
   */
  @Override
  public void setGenerateRanking(boolean doRank) {
    m_rankingRequested = doRank;
  }

  /**
   * Gets whether ranking has been requested. This is used by the
   * AttributeSelection module to determine if rankedAttributes() should be
   * called.
   * 
   * @return true if ranking has been requested.
   */
  @Override
  public boolean getGenerateRanking() {
    return m_rankingRequested;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String startSetTipText() {
    return "Set the start point for the search. This is specified as a comma "
        + "seperated list off attribute indexes starting at 1. It can include "
        + "ranges. Eg. 1,2,5-9,17.";
  }

  /**
   * Sets a starting set of attributes for the search. It is the search method's
   * responsibility to report this start set (if any) in its toString() method.
   * 
   * @param startSet a string containing a list of attributes (and or ranges),
   *          eg. 1,2,6,10-15.
   * @throws Exception if start set can't be set.
   */
  @Override
  public void setStartSet(String startSet) throws Exception {
    m_startRange.setRanges(startSet);
  }

  /**
   * Returns a list of attributes (and or attribute ranges) as a String
   * 
   * @return a list of attributes (and or attribute ranges)
   */
  @Override
  public String getStartSet() {
    return m_startRange.getRanges();
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String conservativeForwardSelectionTipText() {
    return "If true (and forward search is selected) then attributes "
        + "will continue to be added to the best subset as long as merit does "
        + "not degrade.";
  }

  /**
   * Set whether attributes should continue to be added during a forward search
   * as long as merit does not decrease
   * 
   * @param c true if atts should continue to be atted
   */
  public void setConservativeForwardSelection(boolean c) {
    m_conservativeSelection = c;
  }

  /**
   * Gets whether conservative selection has been enabled
   * 
   * @return true if conservative forward selection is enabled
   */
  public boolean getConservativeForwardSelection() {
    return m_conservativeSelection;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String debuggingOutputTipText() {
    return "Output debugging information to the console";
  }

  /**
   * Set whether to output debugging info to the console
   * 
   * @param d true if dubugging info is to be output
   */
  public void setDebuggingOutput(boolean d) {
    m_debug = d;
  }

  /**
   * Get whether to output debugging info to the console
   * 
   * @return true if dubugging info is to be output
   */
  public boolean getDebuggingOutput() {
    return m_debug;
  }

  /**
   * @return a string to describe the option
   */
  public String numExecutionSlotsTipText() {

    return "The number of execution slots, for example, the number of cores in the CPU.";
  }

  /**
   * Gets the number of threads.
   */
  public int getNumExecutionSlots() {

    return m_poolSize;
  }

  /**
   * Sets the number of threads
   */
  public void setNumExecutionSlots(int nT) {

    m_poolSize = nT;
  }

  /**
   * Returns an enumeration describing the available options.
   * 
   * @return an enumeration of all the available options.
   **/
  @Override
  public Enumeration listOptions() {
    Vector newVector = new Vector(5);

    newVector.addElement(new Option("\tUse conservative forward search", "-C",
        0, "-C"));

    newVector.addElement(new Option("\tUse a backward search instead of a"
        + "\n\tforward one.", "-B", 0, "-B"));
    newVector.addElement(new Option("\tSpecify a starting set of attributes."
        + "\n\tEg. 1,3,5-7.", "P", 1, "-P <start set>"));

    newVector.addElement(new Option("\tProduce a ranked list of attributes.",
        "R", 0, "-R"));
    newVector.addElement(new Option("\tSpecify a theshold by which attributes"
        + "\n\tmay be discarded from the ranking."
        + "\n\tUse in conjuction with -R", "T", 1, "-T <threshold>"));

    newVector.addElement(new Option("\tSpecify number of attributes to select",
        "N", 1, "-N <num to select>"));

    newVector.addElement(new Option("\t" + numExecutionSlotsTipText()
        + " (default 1)\n", "-num-slots", 1, "-num-slots <int>"));

    newVector.addElement(new Option("\tPrint debugging output", "D", 0, "-D"));

    return newVector.elements();

  }

  /**
   * Parses a given list of options.
   * <p/>
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -C
   *  Use conservative forward search</pre>
   * 
   * <pre> -B
   *  Use a backward search instead of a
   *  forward one.</pre>
   * 
   * <pre> -P &lt;start set&gt;
   *  Specify a starting set of attributes.
   *  Eg. 1,3,5-7.</pre>
   * 
   * <pre> -R
   *  Produce a ranked list of attributes.</pre>
   * 
   * <pre> -T &lt;threshold&gt;
   *  Specify a theshold by which attributes
   *  may be discarded from the ranking.
   *  Use in conjuction with -R</pre>
   * 
   * <pre> -N &lt;num to select&gt;
   *  Specify number of attributes to select</pre>
   * 
   * <pre> -num-slots &lt;int&gt;
   *  The number of execution slots, for example, the number of cores in the CPU. (default 1)
   * </pre>
   * 
   * <pre> -D
   *  Print debugging output</pre>
   * 
   <!-- options-end -->
   * 
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {
    String optionString;
    resetOptions();

    setSearchBackwards(Utils.getFlag('B', options));

    setConservativeForwardSelection(Utils.getFlag('C', options));

    optionString = Utils.getOption('P', options);
    if (optionString.length() != 0) {
      setStartSet(optionString);
    }

    setGenerateRanking(Utils.getFlag('R', options));

    optionString = Utils.getOption('T', options);
    if (optionString.length() != 0) {
      Double temp;
      temp = Double.valueOf(optionString);
      setThreshold(temp.doubleValue());
    }

    optionString = Utils.getOption('N', options);
    if (optionString.length() != 0) {
      setNumToSelect(Integer.parseInt(optionString));
    }

    optionString = Utils.getOption("num-slots", options);
    if (optionString.length() > 0) {
      setNumExecutionSlots(Integer.parseInt(optionString));
    }

    setDebuggingOutput(Utils.getFlag('D', options));
  }

  /**
   * Gets the current settings of ReliefFAttributeEval.
   * 
   * @return an array of strings suitable for passing to setOptions()
   */
  @Override
  public String[] getOptions() {
    String[] options = new String[12];
    int current = 0;

    if (getSearchBackwards()) {
      options[current++] = "-B";
    }

    if (getConservativeForwardSelection()) {
      options[current++] = "-C";
    }

    if (!(getStartSet().equals(""))) {
      options[current++] = "-P";
      options[current++] = "" + startSetToString();
    }

    if (getGenerateRanking()) {
      options[current++] = "-R";
    }
    options[current++] = "-T";
    options[current++] = "" + getThreshold();

    options[current++] = "-N";
    options[current++] = "" + getNumToSelect();

    options[current++] = "-num-slots";
    options[current++] = "" + getNumExecutionSlots();

    if (getDebuggingOutput()) {
      options[current] = "-D";
    }

    while (current < options.length) {
      options[current++] = "";
    }
    return options;
  }

  /**
   * converts the array of starting attributes to a string. This is used by
   * getOptions to return the actual attributes specified as the starting set.
   * This is better than using m_startRanges.getRanges() as the same start set
   * can be specified in different ways from the command line---eg 1,2,3 == 1-3.
   * This is to ensure that stuff that is stored in a database is comparable.
   * 
   * @return a comma seperated list of individual attribute numbers as a String
   */
  protected String startSetToString() {
    StringBuffer FString = new StringBuffer();
    boolean didPrint;

    if (m_starting == null) {
      return getStartSet();
    }
    for (int i = 0; i < m_starting.length; i++) {
      didPrint = false;

      if ((m_hasClass == false) || (m_hasClass == true && i != m_classIndex)) {
        FString.append((m_starting[i] + 1));
        didPrint = true;
      }

      if (i == (m_starting.length - 1)) {
        FString.append("");
      } else {
        if (didPrint) {
          FString.append(",");
        }
      }
    }

    return FString.toString();
  }

  /**
   * returns a description of the search.
   * 
   * @return a description of the search as a String.
   */
  @Override
  public String toString() {
    StringBuffer FString = new StringBuffer();
    FString.append("\tGreedy Stepwise ("
        + ((m_backward) ? "backwards)" : "forwards)") + ".\n\tStart set: ");

    if (m_starting == null) {
      if (m_backward) {
        FString.append("all attributes\n");
      } else {
        FString.append("no attributes\n");
      }
    } else {
      FString.append(startSetToString() + "\n");
    }
    if (!m_doneRanking) {
      FString.append("\tMerit of best subset found: "
          + Utils.doubleToString(Math.abs(m_bestMerit), 8, 3) + "\n");
    } else {
      if (m_backward) {
        FString
            .append("\n\tRanking is the order that attributes were removed, "
                + "starting \n\twith all attributes. The merit scores in the left"
                + "\n\tcolumn are the goodness of the remaining attributes in the"
                + "\n\tsubset after removing the corresponding in the right column"
                + "\n\tattribute from the subset.\n");
      } else {
        FString
            .append("\n\tRanking is the order that attributes were added, starting "
                + "\n\twith no attributes. The merit scores in the left column"
                + "\n\tare the goodness of the subset after the adding the"
                + "\n\tcorresponding attribute in the right column to the subset.\n");
      }
    }

    if ((m_threshold != -Double.MAX_VALUE) && (m_doneRanking)) {
      FString.append("\tThreshold for discarding attributes: "
          + Utils.doubleToString(m_threshold, 8, 4) + "\n");
    }

    return FString.toString();
  }

  /**
   * Searches the attribute subset space by forward selection.
   * 
   * @param ASEval the attribute evaluator to guide the search
   * @param data the training instances.
   * @return an array (not necessarily ordered) of selected attribute indexes
   * @throws Exception if the search can't be completed
   */
  @Override
  public int[] search(ASEvaluation ASEval, Instances data) throws Exception {

    int i;
    double best_merit = -Double.MAX_VALUE;
    double temp_best, temp_merit;
    int temp_index = 0;
    BitSet temp_group;
    boolean parallel = (m_poolSize > 1);
    if (parallel) {
      m_pool = Executors.newFixedThreadPool(m_poolSize);
    }

    if (data != null) { // this is a fresh run so reset
      resetOptions();
      m_Instances = data;
    }
    m_ASEval = ASEval;

    m_numAttribs = m_Instances.numAttributes();

    if (m_best_group == null) {
      m_best_group = new BitSet(m_numAttribs);
    }

    if (!(m_ASEval instanceof SubsetEvaluator)) {
      throw new Exception(m_ASEval.getClass().getName() + " is not a "
          + "Subset evaluator!");
    }

    m_startRange.setUpper(m_numAttribs - 1);
    if (!(getStartSet().equals(""))) {
      m_starting = m_startRange.getSelection();
    }

    if (m_ASEval instanceof UnsupervisedSubsetEvaluator) {
      m_hasClass = false;
      m_classIndex = -1;
    } else {
      m_hasClass = true;
      m_classIndex = m_Instances.classIndex();
    }

    final SubsetEvaluator ASEvaluator = (SubsetEvaluator) m_ASEval;

    if (m_rankedAtts == null) {
      m_rankedAtts = new double[m_numAttribs][2];
      m_rankedSoFar = 0;
    }

    // If a starting subset has been supplied, then initialise the bitset
    if (m_starting != null && m_rankedSoFar <= 0) {
      for (i = 0; i < m_starting.length; i++) {
        if ((m_starting[i]) != m_classIndex) {
          m_best_group.set(m_starting[i]);
        }
      }
    } else {
      if (m_backward && m_rankedSoFar <= 0) {
        for (i = 0; i < m_numAttribs; i++) {
          if (i != m_classIndex) {
            m_best_group.set(i);
          }
        }
      }
    }

    // Evaluate the initial subset
    best_merit = ASEvaluator.evaluateSubset(m_best_group);

    // main search loop
    boolean done = false;
    boolean addone = false;
    boolean z;

    if (m_debug && parallel) {
      System.err.println("Evaluating subsets in parallel...");
    }
    while (!done) {
      List<Future<Double[]>> results = new ArrayList<Future<Double[]>>();
      temp_group = (BitSet) m_best_group.clone();
      temp_best = best_merit;
      if (m_doRank) {
        temp_best = -Double.MAX_VALUE;
      }
      done = true;
      addone = false;
      for (i = 0; i < m_numAttribs; i++) {
        if (m_backward) {
          z = ((i != m_classIndex) && (temp_group.get(i)));
        } else {
          z = ((i != m_classIndex) && (!temp_group.get(i)));
        }
        if (z) {
          // set/unset the bit
          if (m_backward) {
            temp_group.clear(i);
          } else {
            temp_group.set(i);
          }

          if (parallel) {
            final BitSet tempCopy = (BitSet) temp_group.clone();
            final int attBeingEvaluated = i;

            // make a copy if the evaluator is not thread safe
            final SubsetEvaluator theEvaluator = (ASEvaluator instanceof weka.core.ThreadSafe) ? ASEvaluator
                : (SubsetEvaluator) ASEvaluation.makeCopies(m_ASEval, 1)[0];

            Future<Double[]> future = m_pool.submit(new Callable<Double[]>() {
              @Override
              public Double[] call() throws Exception {
                Double[] r = new Double[2];
                double e = theEvaluator.evaluateSubset(tempCopy);
                r[0] = new Double(attBeingEvaluated);
                r[1] = e;
                return r;
              }
            });

            results.add(future);
          } else {
            temp_merit = ASEvaluator.evaluateSubset(temp_group);
            if (m_backward) {
              z = (temp_merit >= temp_best);
            } else {
              if (m_conservativeSelection) {
                z = (temp_merit >= temp_best);
              } else {
                z = (temp_merit > temp_best);
              }
            }

            if (z) {
              temp_best = temp_merit;
              temp_index = i;
              addone = true;
              done = false;
            }
          }

          // unset this addition/deletion
          if (m_backward) {
            temp_group.set(i);
          } else {
            temp_group.clear(i);
          }
          if (m_doRank) {
            done = false;
          }
        }
      }

      if (parallel) {
        for (int j = 0; j < results.size(); j++) {
          Future<Double[]> f = results.get(j);

          int index = f.get()[0].intValue();
          temp_merit = f.get()[1].doubleValue();

          if (m_backward) {
            z = (temp_merit >= temp_best);
          } else {
            if (m_conservativeSelection) {
              z = (temp_merit >= temp_best);
            } else {
              z = (temp_merit > temp_best);
            }
          }

          if (z) {
            temp_best = temp_merit;
            temp_index = index;
            addone = true;
            done = false;
          }
        }
      }

      if (addone) {
        if (m_backward) {
          m_best_group.clear(temp_index);
        } else {
          m_best_group.set(temp_index);
        }
        best_merit = temp_best;
        if (m_debug) {
          System.err.print("Best subset found so far: ");
          int[] atts = attributeList(m_best_group);
          for (int a : atts) {
            System.err.print("" + (a + 1) + " ");
          }
          System.err.println("\nMerit: " + best_merit);
        }
        m_rankedAtts[m_rankedSoFar][0] = temp_index;
        m_rankedAtts[m_rankedSoFar][1] = best_merit;
        m_rankedSoFar++;
      }
    }

    if (parallel) {
      m_pool.shutdown();
    }

    m_bestMerit = best_merit;
    return attributeList(m_best_group);
  }

  /**
   * Produces a ranked list of attributes. Search must have been performed prior
   * to calling this function. Search is called by this function to complete the
   * traversal of the the search space. A list of attributes and merits are
   * returned. The attributes a ranked by the order they are added to the subset
   * during a forward selection search. Individual merit values reflect the
   * merit associated with adding the corresponding attribute to the subset;
   * because of this, merit values may initially increase but then decrease as
   * the best subset is "passed by" on the way to the far side of the search
   * space.
   * 
   * @return an array of attribute indexes and associated merit values
   * @throws Exception if something goes wrong.
   */
  @Override
  public double[][] rankedAttributes() throws Exception {

    if (m_rankedAtts == null || m_rankedSoFar == -1) {
      throw new Exception("Search must be performed before attributes "
          + "can be ranked.");
    }

    m_doRank = true;
    search(m_ASEval, null);

    double[][] final_rank = new double[m_rankedSoFar][2];
    for (int i = 0; i < m_rankedSoFar; i++) {
      final_rank[i][0] = m_rankedAtts[i][0];
      final_rank[i][1] = m_rankedAtts[i][1];
    }

    resetOptions();
    m_doneRanking = true;

    if (m_numToSelect > final_rank.length) {
      throw new Exception("More attributes requested than exist in the data");
    }

    if (m_numToSelect <= 0) {
      if (m_threshold == -Double.MAX_VALUE) {
        m_calculatedNumToSelect = final_rank.length;
      } else {
        determineNumToSelectFromThreshold(final_rank);
      }
    }

    return final_rank;
  }

  private void determineNumToSelectFromThreshold(double[][] ranking) {
    int count = 0;
    for (int i = 0; i < ranking.length; i++) {
      if (ranking[i][1] > m_threshold) {
        count++;
      }
    }
    m_calculatedNumToSelect = count;
  }

  /**
   * converts a BitSet into a list of attribute indexes
   * 
   * @param group the BitSet to convert
   * @return an array of attribute indexes
   **/
  protected int[] attributeList(BitSet group) {
    int count = 0;

    // count how many were selected
    for (int i = 0; i < m_numAttribs; i++) {
      if (group.get(i)) {
        count++;
      }
    }

    int[] list = new int[count];
    count = 0;

    for (int i = 0; i < m_numAttribs; i++) {
      if (group.get(i)) {
        list[count++] = i;
      }
    }

    return list;
  }

  /**
   * Resets options
   */
  protected void resetOptions() {
    m_doRank = false;
    m_best_group = null;
    m_ASEval = null;
    m_Instances = null;
    m_rankedSoFar = -1;
    m_rankedAtts = null;
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 9848 $");
  }
}

